Cromwell was one of the signatories of King Charles I's death warrant in 1649, and as a member of the Rump Parliament (1649–53) he dominated the short-lived Commonwealth of England. He was selected to take command of the English campaign in Ireland during 1649–50. Cromwell's forces defeated the Confederate and Royalist coalition in Ireland and occupied the country – bringing to an end the Irish Confederate Wars. During this period a series of Penal Laws were passed against Roman Catholics (a significant minority in England and Scotland but the vast majority in Ireland), and a substantial amount of their land was confiscated. Cromwell also led a campaign against the Scottish army between 1650 and 1651.

Cromwell led an Irish and Scottish campaign and it was at that time that many Irish were murdered or shippd off into slavery.

Cromwell led a Parliamentary invasion of Ireland from 1649–50. Parliament's key opposition was the military threat posed by the alliance of the Irish Confederate Catholics and English royalists (signed in 1649). The Confederate-Royalist alliance was judged to be the biggest single threat facing the Commonwealth. However, the political situation in Ireland in 1649 was extremely fractured: there were also separate forces of Irish Catholics who were opposed to the royalist alliance, and Protestant royalist forces that were gradually moving towards Parliament. Cromwell said in a speech to the army Council on 23 March that "I had rather be overthrown by a Cavalierish interest than a Scotch interest; I had rather be overthrown by a Scotch interest than an Irish interest and I think of all this is the most dangerous".[39]

Cromwell's hostility to the Irish was religious as well as political. He was passionately opposed to the Catholic Church, which he saw as denying the primacy of the Bible in favour of papal and clerical authority, and which he blamed for suspected tyranny and persecution of Protestants in Europe.[40] Cromwell's association of Catholicism with persecution was deepened with the Irish Rebellion of 1641. This rebellion, although intended to be bloodless, was marked by massacres of English and Scottish Protestant settlers by Irish and Old English, and Highland Scot Catholics in Ireland. These settlers had settled on land seized from former, native Catholic owners to make way for the non-native Protestants. These factors contributed to the brutality of the Cromwell military campaign in Ireland.[41]

Parliament had planned to re-conquer Ireland since 1641 and had already sent an invasion force there in 1647. Cromwell's invasion of 1649 was much larger and, with the civil war in England over, could be regularly reinforced and re-supplied. His nine-month military campaign was brief and effective, though it did not end the war in Ireland. Before his invasion, Parliamentarian forces held only outposts in Dublin and Derry. When he departed Ireland, they occupied most of the eastern and northern parts of the country. After his landing at Dublin on 15 August 1649 (itself only recently defended from an Irish and English Royalist attack at the Battle of Rathmines), Cromwell took the fortified port towns of Drogheda and Wexford to secure logistical supply from England. At the Siege of Drogheda in September 1649, Cromwell's troops killed nearly 3,500 people after the town's capture—comprising around 2,700 Royalist soldiers and all the men in the town carrying arms, including some civilians, prisoners and Roman Catholic priests.[42][unreliable source?] Cromwell wrote afterwards that:

"I am persuaded that this is a righteous judgment of God upon these barbarous wretches, who have imbued their hands in so much innocent blood and that it will tend to prevent the effusion of blood for the future, which are satisfactory grounds for such actions, which otherwise cannot but work remorse and regret.[43]"

At the Siege of Wexford in October, another massacre took place under confused circumstances. While Cromwell was apparently trying to negotiate surrender terms, some of his soldiers broke into the town, killed 2,000 Irish troops and up to 1,500 civilians, and burned much of the town.[44] No disciplinary actions were taken against his forces subsequent to this second massacre.

After the taking of Drogheda, Cromwell sent a column north to Ulster to secure the north of the country and went on to besiege Waterford, Kilkenny and Clonmel in Ireland's south-east. Kilkenny surrendered on terms, as did many other towns like New Ross and Carlow, but Cromwell failed to take Waterford, and at the siege of Clonmel in May 1650 he lost up to 2,000 men in abortive assaults before the town surrendered.[45]

One of his major victories in Ireland was diplomatic rather than military. With the help of Roger Boyle, 1st Earl of Orrery, Cromwell persuaded the Protestant Royalist troops in Cork to change sides and fight with the Parliament.[46] At this point, word reached Cromwell that Charles II had landed in Scotland and been proclaimed king by the Covenanter regime. Cromwell therefore returned to England from Youghal on 26 May 1650 to counter this threat.[47]

The Parliamentarian conquest of Ireland dragged on for almost three years after Cromwell's departure. The campaigns under Cromwell's successors Henry Ireton and Edmund Ludlow mostly consisted of long sieges of fortified cities and guerrilla warfare in the countryside. The last Catholic-held town, Galway, surrendered in April 1652 and the last Irish troops capitulated in April of the following year.[45]

In the wake of the Commonwealth's conquest, the public practice of Catholicism was banned and Catholic priests were killed when captured.[48][unreliable source?] All Catholic-owned land was confiscated in the Act for the Settlement of Ireland 1652 and given to Scottish and English settlers, the Parliament's financial creditors and Parliamentary soldiers. The remaining Catholic landowners were allocated poorer land in the province of Connacht—this led to the Cromwellian attributed phrase "To hell or to Connacht". Under the Commonwealth, Catholic landownership dropped from 60% of the total to just 8%.

On the other hand, the worst atrocities committed in Ireland, such as mass evictions, killings and deportation of over 50,000 men, women and children as prisoners of war and indentured servants[53] to Bermuda and Barbados, were carried out under the command of other generals after Cromwell had left for England.[54] However other historians would argue that ultimately he was the commander of these generals. Some point to his actions on entering Ireland. Cromwell demanded that no supplies were to be seized from the civilian inhabitants and that everything should be fairly purchased; "I do hereby warn....all Officers, Soldiers and others under my command not to do any wrong or violence toward Country People or any persons whatsoever, unless they be actually in arms or office with the enemy.....as they shall answer to the contrary at their utmost peril." However it should be noted that he landed in Dublin, a city with no Catholic population as they had been previously expelled. Several English soldiers were hanged for disobeying these orders.

While Cromwell was off killing and slaving Irish, he strangely had a yearning to help more Jews come into England and convert them to Christianity.

There was interest in Jewish matters in the leadership of the Commonwealth and
Protectorate for two reasons, one pragmatic and the other doctrinal. The
pragmatic reason was that based on the international trade and commercial
connections of the Amsterdam Jewish community it was recognised that a strong
Jewish presence in London would be advantageous. With flourishing links to the
East and West Indies and to the New World Jewish traders in London could make
the city to Amsterdam as a commercial centre.

The doctrinal reason was
the belief amongst godly Protestants, including Cromwell, that the conversion of
the Jews to Christianity was essential before Christ would return to reign on
earth. 1656 was thought by some to be the actual year in which this would
happen.

What saddens me the most is that most Irish Heritage Centers and sites are completely silent about this past of the Irish people. Why are they silent? The Irish slaves and slaughter must be remembered and talked about.

The commercial policy that led to the Navigation Act in October 1651, made Oliver Cromwell want to attract the rich Jews of Amsterdam to London so that they might transfer their important trade interests with the Spanish Main from Holland to England. The mission of Oliver St John to Amsterdam, though failing to establish a coalition between English and Dutch commercial interests as an alternative to the Navigation Act, had negotiated with Menasseh Ben Israel and the Amsterdam community. A pass was granted to Menasseh to enter England, but he was unable to use it because of the war between England and Holland, which lasted from 1652 to 1654.

As soon as the war ceased, Menasseh Ben Israel sent his brother-in-law, David Abravanel Dormido, to London to present to the council a petition for the readmission of Jews. The council, however, refused to act. Cromwell therefore induced Menasseh himself to come over to London, which he did at the end of September 1655, and there he printed his "humble address" to Cromwell. As a consequence, a national conference was summoned at Whitehall in the early part of December, which included some of the most eminent lawyers, clergymen, and merchants in the country. The lawyers declared no opposition to the Jews' residing in England, but both the clergymen and merchants were opposed to readmission, leading Cromwell to stop the discussion to prevent an adverse decision.

Early in the following year (1656), the question came to a practical issue through the declaration of war against Spain, which resulted in the arrest of Antonio Rodrigues Robles, and forced the Marranos of London to avow their Judaism as a means of avoiding arrest as Spaniards and the confiscation of their goods. As a final result, Cromwell appears to have given informal permission to the Jews to reside and trade in England on condition that they did not obtrude their worship on public notice and that they refrained from making proselytes. Using this permission, Antonio Fernandez Carvajal and Simon de Caceres purchased a piece of land for a Jewish cemetery in 1657, and Solomon Dormido, a nephew of Menasseh Ben Israel, was admitted to the Royal Exchange as a duly licensed broker of the City of London, without taking the usual oath involving a statement of faith in Christianity. Carvajal had previously been granted letters of denization for himself and his son, which guaranteed certain rights of citizenship.